scholarly journals Streptococcus pneumoniae serotypes that frequently colonise the human nasopharynx are common recipients of penicillin-binding protein gene fragments from Streptococcus mitis

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Akuzike Kalizang'oma ◽  
Chrispin Chaguza ◽  
Andrea Gori ◽  
Charlotte Davison ◽  
Sandra Beleza ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Type Species ◽  
Binding Protein ◽  
Pneumococcal Serotypes ◽  
Penicillin Binding Protein ◽  
Beta Lactam ◽  
Streptococcus Mitis ◽  
Content Type ◽  
Link Type ◽  
Close Relatives

Streptococcus pneumoniae is an important global pathogen that causes bacterial pneumonia, sepsis and meningitis. Beta-lactam antibiotics are the first-line treatment for pneumococcal disease, however, their effectiveness is hampered by beta-lactam resistance facilitated by horizontal genetic transfer (HGT) with closely related species. Although interspecies HGT is known to occur among the species of the genus Streptococcus , the rates and effects of HGT between Streptococcus pneumoniae and its close relatives involving the penicillin binding protein (pbp) genes remain poorly understood. Here we applied the fastGEAR tool to investigate interspecies HGT in pbp genes using a global collection of whole-genome sequences of Streptococcus mitis , Streptococcus oralis and S. pneumoniae . With these data, we established that pneumococcal serotypes 6A, 13, 14, 16F, 19A, 19F, 23F and 35B were the highest-ranking serotypes with acquired pbp fragments. S. mitis was a more frequent pneumococcal donor of pbp fragments and a source of higher pbp nucleotide diversity when compared with S. oralis . Pneumococci that acquired pbp fragments were associated with a higher minimum inhibitory concentration (MIC) for penicillin compared with pneumococci without acquired fragments. Together these data indicate that S. mitis contributes to reduced β-lactam susceptibility among commonly carried pneumococcal serotypes that are associated with long carriage duration and high recombination frequencies. As pneumococcal vaccine programmes mature, placing increasing pressure on the pneumococcal population structure, it will be important to monitor the influence of antimicrobial resistance HGT from commensal streptococci such as S. mitis .

Chitinophaga oryzae sp. nov., an epiphytic bacterium isolated from rice root surfaces

2021 ◽  
Vol 71 (7) ◽  
Author(s):  
Nantawan Niemhom ◽  
Chanwit Suriyachadkun ◽  
Chokchai Kittiwongwattana
Keyword(s):  
Type Species ◽  
Rrna Gene ◽  
Major Polar Lipid ◽  
Bacterial Strains ◽  
Respiratory Quinone ◽  
Content Type ◽  
Link Type ◽  
Major Respiratory Quinone ◽  
Phylogenomic Analyses ◽  
Close Relatives

Two Gram-stain-negative, non-motile, rod-shaped bacterial strains were isolated from the surfaces of rice roots. They were designated as strains 1303T and 1310. Their colonies were circular, entire, opaque, convex and yellow. They were chitinase- and catalase-positive, reduced nitrate and grew at 16–37 °C (optimum, 30 °C), pH 5.0–10.0 (optimum, pH 7.0) and 0–2.0% NaCl (optimum, 1.0 %). Based on the 16S rRNA gene sequence analysis, they were classified as members of the genus Chitinophaga . Results of phylogenetic and phylogenomic analyses indicated that they formed a cluster with Chitinophaga eiseniae YC6729T, Chitinophaga qingshengii JN246T, Chitinophaga varians 10-7 W-9003T and Chitinophaga fulva G-6-1-13T. When the genomic sequences of strains 1303T and 1310 were compared with their close relatives, the average nucleotide identity and digital DNA–DNA hybridization values were below the cut-off levels. Phosphatidylethanolamine was the major polar lipid. MK-7 was the major respiratory quinone. iso-C15 : 0, C16 : 1  ω5c, iso-C17 : 0 3-OH and summed feature 3 (C16 : 1  ω7c/C16 : 1  ω6c) were the predominant fatty acids. Differential characteristics between both strains and their close relatives were also observed. Based on the distinctions in genotypic, phenotypic and chemotypic features, strains 1303T and 1310 represent members of a novel species of the genus Chitinophaga , for which the name Chitinophaga oryzae sp. nov. is proposed. The type strain is 1303T (=KACC 22075T=TBRC 12926T).

scholarly journals A Low-Affinity Penicillin-Binding Protein 2x Variant Is Required for Heteroresistance in Streptococcus pneumoniae

2014 ◽  
Vol 58 (7) ◽  
pp. 3934-3941 ◽  
Author(s):  
Hansjürg Engel ◽  
Moana Mika ◽  
Dalia Denapaite ◽  
Regine Hakenbeck ◽  
Kathrin Mühlemann ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Abc Transporter ◽  
Binding Protein ◽  
Population Analysis ◽  
Resistance Testing ◽  
Penicillin Binding Protein ◽  
Secondary Resistance ◽  
Content Type ◽  
Abc Transporter Genes

ABSTRACTHeteroresistance to penicillin inStreptococcus pneumoniaeis the ability of subpopulations to grow at a higher antibiotic concentration than expected from the MIC. This may render conventional resistance testing unreliable and lead to therapeutic failure. We investigated the role of the primary β-lactam resistance determinants, penicillin-binding protein 2b (PBP2b) and PBP2x, and the secondary resistance determinant PBP1a in heteroresistance to penicillin. Transformants containing PBP genes from the heteroresistant strain Spain23F2349in the nonheteroresistant strain R6 background were tested for heteroresistance by population analysis profiling (PAP). We found thatpbp2x, but notpbp2borpbp1aalone, conferred heteroresistance to R6. However, a change ofpbp2xexpression was not observed, and therefore, expression does not correlate with an increased proportion of resistant subpopulations. In addition, the influence of the CiaRH system, mediating PBP-independent β-lactam resistance, was assessed by PAP onciaRdisruption mutants but revealed no heteroresistant phenotype. We also showed that the highly resistant subpopulations (HOM*) of transformants containing low-affinitypbp2xundergo an increase in resistance upon selection on penicillin plates that partially reverts after passaging on selection-free medium. Shotgun proteomic analysis showed an upregulation of phosphate ABC transporter subunit proteins encoded bypstS,phoU,pstB, andpstCin these highly resistant subpopulations. In conclusion, the presence of low-affinitypbp2xenables certain pneumococcal colonies to survive in the presence of β-lactams. Upregulation of phosphate ABC transporter genes may represent a reversible adaptation to antibiotic stress.

scholarly journals Azithromycin resistance mutations in Streptococcus pneumoniae as revealed by a chemogenomic screen

2020 ◽  
Vol 6 (11) ◽  
Author(s):  
Hélène Gingras ◽  
Kévin Patron ◽  
Philippe Leprohon ◽  
Marc Ouellette
Keyword(s):  
Streptococcus Pneumoniae ◽  
Ribosomal Proteins ◽  
Type Species ◽  
Chemical Mutagenesis ◽  
Resistance Mutations ◽  
Content Type ◽  
Link Type ◽  
Chromosomal Changes ◽  
23S Ribosomal Rna ◽  
Ribosomal Binding Site

We report on the combination of chemical mutagenesis, azithromycin selection and next-generation sequencing (Mut-Seq) for the identification of small nucleotide variants that decrease the susceptibility of Streptococcus pneumoniae to the macrolide antibiotic azithromycin. Mutations in the 23S ribosomal RNA or in ribosomal proteins can confer resistance to macrolides and these were detected by Mut-Seq. By concentrating on recurrent variants, we could associate mutations in genes implicated in the metabolism of glutamine with decreased azithromycin susceptibility among S. pneumoniae mutants. Glutamine synthetase catalyses the transformation of glutamate and ammonium into glutamine and its chemical inhibition is shown to sensitize S. pneumoniae to antibiotics. A mutation affecting the ribosomal-binding site of a putative ribonuclease J2 is also shown to confer low-level resistance. Mut-Seq has the potential to reveal chromosomal changes enabling high resistance as well as novel events conferring more subtle phenotypes.

scholarly journals Emergence of Ceftriaxone Resistance during a Case of Pneumococcal Meningitis with Fatal Evolution

2019 ◽  
Vol 64 (3) ◽  
Author(s):  
A. Mizrahi ◽  
J. C. Marvaud ◽  
B. Pilmis ◽  
J. C. Nguyen Van ◽  
C. Couzigou ◽  
...  
Keyword(s):  
Cerebrospinal Fluid ◽  
Streptococcus Pneumoniae ◽  
Pneumococcal Meningitis ◽  
Binding Protein ◽  
Third Generation ◽  
Penicillin Binding Protein ◽  
Content Type ◽  
Neurological Improvement ◽  
Third Generation Cephalosporins ◽  
Fatal Evolution

ABSTRACT We report a case of a 62-year-old man treated for Streptococcus pneumoniae meningitis by ceftriaxone and dexamethasone. After neurological improvement, neurological degradation by vasculitis occurred, despite effective concentrations of ceftriaxone in the serum and cerebrospinal fluid (CSF). S. pneumoniae with increased MICs to third-generation-cephalosporins (3GC) was isolated from the ventricular fluid 10 days after the isolation of the first strain. Isolate analysis showed that a mutation in the penicillin-binding protein 2X (PBP2X) has occurred under treatment.

Youngiibacter fragilis gen. nov., sp. nov., isolated from natural gas production-water and reclassification of Acetivibrio multivorans as Youngiibacter multivorans comb. nov.

2014 ◽  
Vol 64 (Pt_1) ◽  
pp. 198-205 ◽  
Author(s):  
Paul A. Lawson ◽  
Boris Wawrik ◽  
Toby D. Allen ◽  
Crystal N. Johnson ◽  
Christopher R. Marks ◽  
...  
Keyword(s):  
Natural Gas ◽  
Type Species ◽  
Gas Production ◽  
Rrna Gene ◽  
The Novel ◽  
Natural Gas Production ◽  
Content Type ◽  
Link Type ◽  
Production Water ◽  
Close Relatives

A taxonomic study employing a polyphasic approach was performed on a novel anaerobic bacterium isolated from natural gas production-water. The bacterium stained Gram-negative and consisted of non-motile, non-spore-forming, rod-shaped cells. Products of glucose or starch fermentation were ethanol, CO2, formate, acetate and H2. The predominant fatty acids were C16 : 0 ALDE and summed feature 3 comprising C16 : 1ω7c and/or C16 : 1ω6c. The DNA G+C content was 45.5 mol%. 16S rRNA gene sequence analysis demonstrated that the nearest phylogenetic neighbours of the novel strain were Acetivibrio multivorans DSM 6139T (98.5 %) and Proteiniclasticum ruminis JCM 14817T (95.4 %). The DNA–DNA hybridization value between the novel organism and Acetivibrio multivorans PeC1 DSM 6139T was determined to be only 30.2 %, demonstrating the separateness of the two species. Based on phylogenetic, phenotypic and chemotaxonomic evidence that clearly distinguished strain 232.1T from Proteiniclasticum ruminis and other close relatives, it is proposed that the novel isolate be classified as representing a novel species of a new genus within the family Clostridiaceae , Youngiibacter fragilis gen. nov., sp. nov. The type strain of the type species is 232.1T ( = ATCC BAA-2257T = DSM 24749T). In addition, Acetivibrio multivorans is proposed to be reclassified as Youngiibacter multivorans comb. nov.

scholarly journals Streptococcus pneumoniae, S. pyogenes and S. agalactiae membrane phospholipid remodelling in response to human serum

Microbiology ◽  
2021 ◽  
Vol 167 (5) ◽  
Author(s):  
Luke R. Joyce ◽  
Ziqiang Guan ◽  
Kelli L. Palmer
Keyword(s):  
Streptococcus Pneumoniae ◽  
Human Serum ◽  
Type Species ◽  
Cellular Membrane ◽  
Defined Medium ◽  
Content Type ◽  
Link Type ◽  
Streptococcal Species ◽  
Group A ◽  
Group B

Streptococcus pneumoniae , S. pyogenes (Group A Streptococcus ; GAS) and S. agalactiae (Group B Streptococcus ; GBS) are major aetiological agents of diseases in humans. The cellular membrane, a crucial site in host–pathogen interactions, is poorly characterized in streptococci. Moreover, little is known about whether or how environmental conditions influence their lipid compositions. Using normal phase liquid chromatography coupled with electrospray ionization MS, we characterized the phospholipids and glycolipids of S. pneumoniae , GAS and GBS in routine undefined laboratory medium, streptococcal defined medium and, in order to mimic the host environment, defined medium supplemented with human serum. In human serum-supplemented medium, all three streptococcal species synthesize phosphatidylcholine (PC), a zwitterionic phospholipid commonly found in eukaryotes but relatively rare in bacteria. We previously reported that S. pneumoniae utilizes the glycerophosphocholine (GPC) biosynthetic pathway to synthesize PC. Through substrate tracing experiments, we confirm that GAS and GBS scavenge lysoPC, a major metabolite in human serum, thereby using an abbreviated GPC pathway for PC biosynthesis. Furthermore, we found that plasmanyl-PC is uniquely present in the GBS membrane during growth with human serum, suggesting GBS possesses unusual membrane biochemical or biophysical properties. In summary, we report cellular lipid remodelling by the major pathogenic streptococci in response to metabolites present in human serum.

scholarly journals Pneumococcal serotypes causing non-invasive pneumonia in adults from a South Indian tertiary care hospital and the impact of the newer conjugate vaccines

2021 ◽  
Vol 3 (12) ◽  
Author(s):  
Rosemol Varghese ◽  
Binesh Lal Yesudhason ◽  
Leena Robinson Vimala ◽  
Ayyanraj Neeravi ◽  
Kavipriya Anandhan ◽  
...  
Keyword(s):  
Type Species ◽  
Pneumococcal Pneumonia ◽  
Pneumococcal Vaccines ◽  
Care Hospital ◽  
Pneumococcal Serotypes ◽  
Radiological Findings ◽  
Conjugate Vaccines ◽  
Content Type ◽  
Non Invasive ◽  
Link Type

Background. Streptococcus pneumoniae is the leading cause of community-acquired pneumonia (CAP) in adults. Ageing, chronic conditions and comorbidities are important risk factors for pneumococcal pneumonia. Purpose. There is lack of data on the pneumococcal serotypes causing non-invasive pneumonia in India. This study aims to determine the prevalent pneumococcal serotypes causing non-invasive pneumonia, the associated comorbidities, and the coverage of both the available pneumococcal vaccines in India and conjugate vaccines that are currently undergoing clinical trials. Methods. A total of 280 subjects (aged >16 years) who had clinical symptoms correlating with radiological findings for non-invasive bacteremic pneumonia and microbiological evidence of S. pneumoniae between 2018 and 2020 were included. The clinical, demographic, radiological and microbiological findings were retrieved from the Hospital Information System (HIS). Results. The common serotypes in order of prevalence were 19F, 9V, 23F, 6B, 11A, 13, 34, 10A, 19A and 6A. The predominant non-vaccine serotypes were 13, 34, 35B, 31 and 16F. The associated radiological findings were pneumonic consolidation and multi-lobar involvement. Other coinfected bacterial pathogens included H. influenzae, S. aureus, K. pneumoniae and P. aeruginosa. Conclusion. The pneumococcal vaccines: PCV10/GSK, PCV10/SII, PCV13, PCV15, PCV20 and PPSV23 provide an overall serotype coverage of 36, 41, 47, 48, 61 and 69 %, respectively of S. pneumoniae causing non-invasive pneumonia in South India. Increasing catch-up vaccination using PCV10(SII) in pre-school children could have a more significant impact on reducing pneumococcal pneumonia in adults (>50 years) in terms of increased herd immunity at an affordable cost.

scholarly journals Co-infection in critically ill patients with COVID-19: an observational cohort study from England

2021 ◽  
Vol 70 (4) ◽  
Author(s):  
Vadsala Baskaran ◽  
Hannah Lawrence ◽  
Louise E. Lansbury ◽  
Karmel Webb ◽  
Shahideh Safavi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Cohort Study ◽  
Streptococcus Pneumoniae ◽  
Critically Ill ◽  
Type Species ◽  
Severe Illness ◽  
Gram Negative ◽  
Content Type ◽  
Link Type ◽  
Icu Stay

Introduction. During previous viral pandemics, reported co-infection rates and implicated pathogens have varied. In the 1918 influenza pandemic, a large proportion of severe illness and death was complicated by bacterial co-infection, predominantly Streptococcus pneumoniae and Staphylococcus aureus . Gap statement. A better understanding of the incidence of co-infection in patients with COVID-19 infection and the pathogens involved is necessary for effective antimicrobial stewardship. Aim. To describe the incidence and nature of co-infection in critically ill adults with COVID-19 infection in England. Methodology. A retrospective cohort study of adults with COVID-19 admitted to seven intensive care units (ICUs) in England up to 18 May 2020, was performed. Patients with completed ICU stays were included. The proportion and type of organisms were determined at <48 and >48 h following hospital admission, corresponding to community and hospital-acquired co-infections. Results. Of 254 patients studied (median age 59 years (IQR 49–69); 64.6 % male), 139 clinically significant organisms were identified from 83 (32.7 %) patients. Bacterial co-infections/ co-colonisation were identified within 48 h of admission in 14 (5.5 %) patients; the commonest pathogens were Staphylococcus aureus (four patients) and Streptococcus pneumoniae (two patients). The proportion of pathogens detected increased with duration of ICU stay, consisting largely of Gram-negative bacteria, particularly Klebsiella pneumoniae and Escherichia coli . The co-infection/ co-colonisation rate >48 h after admission was 27/1000 person-days (95 % CI 21.3–34.1). Patients with co-infections/ co-colonisation were more likely to die in ICU (crude OR 1.78,95 % CI 1.03–3.08, P=0.04) compared to those without co-infections/ co-colonisation. Conclusion. We found limited evidence for community-acquired bacterial co-infection in hospitalised adults with COVID-19, but a high rate of Gram-negative infection acquired during ICU stay.

scholarly journals New Insights into Beta-Lactam Resistance of Streptococcus pneumoniae: Serine Protease HtrA Degrades Altered Penicillin-Binding Protein 2x

2021 ◽  
Vol 9 (8) ◽  
pp. 1685
Author(s):  
Katharina Peters ◽  
Inga Schweizer ◽  
Regine Hakenbeck ◽  
Dalia Denapaite
Keyword(s):  
Streptococcus Pneumoniae ◽  
Serine Protease ◽  
Response Regulator ◽  
Binding Protein ◽  
Penicillin Binding Protein ◽  
Beta Lactam ◽  
Kinase Gene ◽  
Protein Kinase Gene ◽  
Cognate Response Regulator ◽  
Post Transcriptional Regulation

Reduced amounts of the essential penicillin-binding protein 2x (PBP2x) were detected in two cefotaxime-resistant Streptococcus pneumoniae laboratory mutants C405 and C606. These mutants contain two or four mutations in the penicillin-binding domain of PBP2x, respectively. The transcription of the pbp2x gene was not affected in both mutants; thus, the reduced PBP2x amounts were likely due to post-transcriptional regulation. The mutants carry a mutation in the histidine protein kinase gene ciaH, resulting in enhanced gene expression mediated by the cognate response regulator CiaR. Deletion of htrA, encoding a serine protease regulated by CiaR, or inactivation of HtrA proteolytic activity showed that HtrA is indeed responsible for PBP2x degradation in both mutants, and that this affects β-lactam resistance. Depletion of the PBP2xC405 in different genetic backgrounds confirmed that HtrA degrades PBP2xC405. A GFP-PBP2xC405 fusion protein still localized at the septum in the absence of HtrA. The complementation studies in HtrA deletion strains showed that HtrA can be overexpressed in pneumococcal cells to specific levels, depending on the genetic background. Quantitative Western blotting revealed that the PBP2x amount in C405 strain was less than 20% compared to parental strain, suggesting that PBP2x is an abundant protein in S. pneumoniae R6 strain.

scholarly journals A comparative study of pan-genome methods for microbial organisms: Acinetobacter baumannii pan-genome reveals structural variation in antimicrobial resistance-carrying plasmids

2021 ◽  
Vol 7 (11) ◽  
Author(s):  
Aysun Urhan ◽  
Thomas Abeel
Keyword(s):  
Acinetobacter Baumannii ◽  
Type Species ◽  
Variant Calling ◽  
Reference Sequence ◽  
Beta Lactam ◽  
Final Size ◽  
Content Type ◽  
Pan Genome ◽  
Link Type ◽  
Microbial Organisms

Microbial organisms have diverse populations, where using a single linear reference sequence in comparative studies introduces reference-bias in downstream analyses, and leads to a failure to account for variability in the population. Recently, pan-genome graphs have emerged as an alternative to the traditional linear reference with many successful applications and a rapid increase in the number of methods available in the literature. Despite this enthusiasm, there has been no attempt at exploring these graph construction methods in depth, demonstrating their practical use. In this study, we aim to develop a general guide to help researchers who may want to incorporate pan-genomes in their analyses of microbial organisms. We evaluated the state-of-the art pan-genome construction tools to model a collection of 70 Acinetobacter baumannii strains. Our results suggest that all tools produced pan-genome graphs conforming to our expectations based on previous literature, and that their approach to homologue detection is likely to be the most influential in determining the final size and complexity of the pan-genome. The graphs overlapped most in the core pan-genome content while the cloud genes varied significantly among tools. We propose an alternative approach for pan-genome construction by combining two of the tools, Panaroo and Ptolemy, to further exploit them in downstream analyses, and demonstrate the effectiveness of our pipeline for structural variant calling in beta-lactam resistance genes in the same set of A. baumannii isolates, identifying various transposon structures for carbapenem resistance in chromosome, as well as plasmids. We identify a novel plasmid structure in two multidrug-resistant clinical isolates that had previously been studied, and which could be important for their resistance phenotypes.

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